[DFTB-Plus-User] Treatment of Imaginary Frequencies (rsaha at icredd.hokudai.ac.jp)
rsaha at icredd.hokudai.ac.jp
rsaha at icredd.hokudai.ac.jp
Sat Jan 29 02:42:38 CET 2022
Hello Bálint,
Thank you for your reply.
I was also thinking to leave them as it as the imaginary frequencies are
very low. But I was not sure to do this.
I am showing a few more frequencies (total of 1950 frequencies) are as
follows,
Vibrational modes (cm-1):
1 -2.09
2 -1.02
3 -0.00
4 0.00
5 0.00
6 4.94
7 5.84
8 6.56
9 6.71
10 7.09
11 9.26
12 11.24
13 12.05
14 12.18
15 12.42
16 13.23
.. ..
.. ..
181 97.80
182 100.02
183 100.22
184 101.85
.. ..
.. ..
1946 3028.11
1947 3028.13
1948 3028.15
1949 3028.50
1950 3029.22
Is it okay to consider them as significantly high and consider this
geometry for further calculation?
Regards
Ranajit
----- Original Message -----
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Sent Date: 17:17:28 Fri January 28, 2022
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> Today's Topics:
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> 1. error with ELSI solvers (Huy Pham)
> 2. Treatment of Imaginary Frequencies (rsaha at icredd.hokudai.ac.jp)
> 3. Re: error with ELSI solvers (Bálint Aradi)
> 4. Re: Treatment of Imaginary Frequencies (Bálint Aradi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 27 Jan 2022 16:58:00 -0800
> From: Huy Pham <pchuy1906 at gmail.com>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: [DFTB-Plus-User] error with ELSI solvers
> Message-ID:
> <CAM1TSkeVrvmGVe-eGEE_A3VbR=sb_CEwQuDy+7AK9rEahi+5Wg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi All,
>
> I have a problem when running short MD simulation using DFTB plus with
> different solvers in ELSI. I used the 3ob dataset, the system is a
> molecular crystal (C, H, N, O) with 576 atoms (supercell).
>
> The simulation was fine with ELPA, but if I changed the solver to OMM
or
> NTPoly, the simulations crashed after finishing the first SCF. The
error is
> "SIGSEGV, segmentation fault occurred" which is difficult to track
down.
>
> When using PEXSI, the error is below:
> **Error! MPI task 38 in elsi_dm_complex_sparse: Number of MPI
tasks
> per pole too small
> **Error! MPI task 270 in elsi_dm_complex_sparse: Number of MPI
tasks
> per pole too small
> **Error! MPI task 3 in elsi_dm_complex_sparse: Number of MPI
tasks
> per pole too small
> **Error! MPI task 219 in elsi_dm_complex_sparse: Number of MPI
tasks
> per pole too small
> I couldn't find any related info in the manual. According to the error
> message, I have tried to increase the number of MPI tasks, still
waiting
> for the simulation to run. Reducing the number of poles doesn't help,
as at
> some point, the error "Too few PEXSI poles" will happen.
>
> Any suggestion would be appreciated!
>
> Thanks,
> Huy
>
> --
>
> C. Huy Pham, Ph.D.
>
> Staff Scientist
>
> Lawrence Livermore National Laboratory
>
> Physical and Life Sciences Directorate
>
> Materials Science Division, L-287
>
> 7000 East Ave, Livermore, CA 94550
> Phone: (925) 422-7881
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> ------------------------------
>
> Message: 2
> Date: Fri, 28 Jan 2022 11:48:03 +0900
> From: <rsaha at icredd.hokudai.ac.jp>
> To: <dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: [DFTB-Plus-User] Treatment of Imaginary Frequencies
> Message-ID:
> <20220128024803.003A538C.0411 at HINES-WebMail.hines.hokudai.ac.jp>
> Content-Type: text/plain; charset=US-ASCII
>
> Hello everyone,
>
> I have a query about the small imaginary frequencies in the DFTB
> computations.
>
> I am doing frequency (SCCTolerance = 1e-8 & RemoveTranslation = Yes)
> calculations after optimisation of the unit cells. The unit cells have
~
> 600 atoms. There are a few imaginary frequencies (as shown below for
two
> different systems) that occurred which are very small.
>
> Vibrational modes (cm-1):
> 1 -1.46
> 2 -0.00
> 3 -0.00
> 4 0.00
> 5 7.40
> 6 7.41
>
> OR
>
> Vibrational modes (cm-1):
> 1 -2.09
> 2 -1.02
> 3 -0.00
> 4 0.00
> 5 0.00
> 6 4.94
>
> In this condition, should I need to remove these imaginary frequencies?
>
> Thank you.
> Regards
> Ranajit
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 28 Jan 2022 09:12:15 +0100
> From: Bálint Aradi <aradi at uni-bremen.de>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] error with ELSI solvers
> Message-ID: <1918135a-4039-4a9b-f51a-75608119a608 at uni-bremen.de>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear Huy,
>
> For the segfault: Often a limited stack size is the reason (hits me
> often). Could you check, whether that is the case? (ulimit -s
unlimited)
>
> As for the PEXSI problem. The error message is generated by the PEXSI
> library within ELSI. I am definitely not a PEXSI expert, but having a
> quick look at the PEXSI code in ELSI
>
> https://gitlab.com/ElectronicStructureLibrary/elsi-interface/-/blob/master/src/elsi_util.f90#L423
>
> suggests, that the product of the number of poles per process
> (ProcsPerPole), the number of poles (Poles) and the number of
processors
> used to search the Fermi level (muPoints) should be greater or equal
> than the number of the MPI processes.
>
> I hope this helps.
>
> Best regards,
>
> BálintBest regards,
>
> Bálint
>
>
>
> On 28.01.22 01:58, Huy Pham wrote:
> > Hi All,
> >
> > I have a problem when running short MD simulation using DFTB plus
with
> > different solvers in ELSI. I used the 3ob dataset, the system is a
> > molecular crystal (C, H, N, O) with 576 atoms (supercell).
> >
> > The simulation was fine with ELPA, but if I changed the solver to
OMM or
> > NTPoly, the simulations crashed after finishing the first SCF. The
error
> > is "SIGSEGV, segmentation fault occurred" which is difficult to
track down.
> >
> > When using PEXSI, the error is below:
> > **Error! MPI task 38 in elsi_dm_complex_sparse: Number of MPI
tasks
> > per pole too small
> > **Error! MPI task 270 in elsi_dm_complex_sparse: Number of MPI
tasks
> > per pole too small
> > **Error! MPI task 3 in elsi_dm_complex_sparse: Number of MPI
tasks
> > per pole too small
> > **Error! MPI task 219 in elsi_dm_complex_sparse: Number of MPI
tasks
> > per pole too small
> > I couldn't find any related info in the manual. According to the
error
> > message, I have tried to increase the number of MPI tasks, still
waiting
> > for the simulation to run. Reducing the number of poles doesn't help,
as
> > at some point, the error "Too few PEXSI poles" will happen.
> >
> > Any suggestion would be appreciated!
> >
> > Thanks,
> > Huy
> >
> > --
> >
> > C. Huy Pham, Ph.D.
> >
> > Staff Scientist
> >
> > Lawrence Livermore National Laboratory
> >
> > Physical and Life Sciences Directorate
> >
> > Materials Science Division, L-287
> >
> > 7000 East Ave, Livermore, CA 94550
> >
> > Phone: (925) 422-7881
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
>
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of
Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
>
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> ------------------------------
>
> Message: 4
> Date: Fri, 28 Jan 2022 09:17:25 +0100
> From: Bálint Aradi <aradi at uni-bremen.de>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] Treatment of Imaginary Frequencies
> Message-ID: <392d3db8-b55b-e52b-c618-5863b733425b at uni-bremen.de>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Dear Ranajit,
>
> I would guess, that those very low frequencies appear because of very
> small residual forces in the system. If all other frequencies (7 and
> above) are significantly higher, I won't probably worry about it.
>
> Best regards,
>
> Bálint
>
> On 28.01.22 03:48, rsaha at icredd.hokudai.ac.jp wrote:
> > Hello everyone,
> >
> > I have a query about the small imaginary frequencies in the DFTB
> > computations.
> >
> > I am doing frequency (SCCTolerance = 1e-8 & RemoveTranslation = Yes)
> > calculations after optimisation of the unit cells. The unit cells
have ~
> > 600 atoms. There are a few imaginary frequencies (as shown below for
two
> > different systems) that occurred which are very small.
> >
> > Vibrational modes (cm-1):
> > 1 -1.46
> > 2 -0.00
> > 3 -0.00
> > 4 0.00
> > 5 7.40
> > 6 7.41
> >
> > OR
> >
> > Vibrational modes (cm-1):
> > 1 -2.09
> > 2 -1.02
> > 3 -0.00
> > 4 0.00
> > 5 0.00
> > 6 4.94
> >
> > In this condition, should I need to remove these imaginary
frequencies?
> >
> > Thank you.
> > Regards
> > Ranajit
> >
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
>
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of
Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
>
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